Suhaib Mohammed
| Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019) |
| URL: https://git.bioconductor.org/packages/ArrayExpress |
| Branch: RELEASE_3_8 |
| Last Commit: f550d15 |
| Last Changed Date: 2018-10-30 11:41:44 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-13 11:20:49 -0400 (Sat, 13 Apr 2019).
| Package 69/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| ArrayExpress 1.42.0 Suhaib Mohammed
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: ArrayExpress |
| Version: 1.42.0 |
| Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ArrayExpress.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings ArrayExpress_1.42.0.tar.gz |
| StartedAt: 2019-04-13 00:32:04 -0400 (Sat, 13 Apr 2019) |
| EndedAt: 2019-04-13 00:37:26 -0400 (Sat, 13 Apr 2019) |
| EllapsedTime: 322.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ArrayExpress.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ArrayExpress.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings ArrayExpress_1.42.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/ArrayExpress.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ArrayExpress/DESCRIPTION' ... OK
* this is package 'ArrayExpress' version '1.42.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'ArrayExpress' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
ae2bioc: no visible global function definition for 'new'
extract.zip : <anonymous>: no visible global function definition for
'unzip'
getAE : <anonymous>: no visible global function definition for
'download.file'
getAE: no visible global function definition for 'download.file'
getDataColsForAE1: no visible global function definition for
'read.table'
preparePhenoDataFor2channel: no visible global function definition for
'new'
queryAE: no visible global function definition for 'download.file'
readDerivedDataFiles: no visible global function definition for
'read.table'
readDerivedDataFiles: no visible global function definition for 'new'
readDerivedDataMatrixFile: no visible global function definition for
'read.table'
readDerivedDataMatrixFile: no visible global function definition for
'new'
readExperimentData: no visible global function definition for 'new'
readFeatures: no visible global function definition for 'read.table'
readFeatures: no visible global function definition for 'new'
readPhenoData: no visible global function definition for 'new'
Undefined global functions or variables:
download.file new read.table unzip
Consider adding
importFrom("methods", "new")
importFrom("utils", "download.file", "read.table", "unzip")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
ArrayExpress 8.65 0.88 17.67
getAE 3.37 0.23 7.98
queryAE 2.61 0.27 11.39
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
ArrayExpress 7.75 0.66 12.63
queryAE 3.16 0.07 11.69
getAE 2.64 0.28 7.35
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.8-bioc/meat/ArrayExpress.Rcheck/00check.log'
for details.
ArrayExpress.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/ArrayExpress_1.42.0.tar.gz && rm -rf ArrayExpress.buildbin-libdir && mkdir ArrayExpress.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ArrayExpress.buildbin-libdir ArrayExpress_1.42.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL ArrayExpress_1.42.0.zip && rm ArrayExpress_1.42.0.tar.gz ArrayExpress_1.42.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 41613 100 41613 0 0 990k 0 --:--:-- --:--:-- --:--:-- 1069k
install for i386
* installing *source* package 'ArrayExpress' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'ArrayExpress'
finding HTML links ... done
ArrayExpress html
ae2bioc html
extract.zip html
getAE html
getcolproc html
getcolraw html
procset html
queryAE html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'ArrayExpress' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ArrayExpress' as ArrayExpress_1.42.0.zip
* DONE (ArrayExpress)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'ArrayExpress' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
ArrayExpress.Rcheck/examples_i386/ArrayExpress-Ex.timings
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ArrayExpress.Rcheck/examples_x64/ArrayExpress-Ex.timings
|